Abstract 5105: Comparing comprehensive NGS panel(s) based approach versus tissue whole exome sequencing (WES) using matched tissue and circulating tumor DNA from late-stage colorectal cancer patients
Authors: Dennis O'Rourke, Roman Alpatov, Danyi Wang, Zheng Feng, Juergen Scheuenpflug
Journal: Cancer Research (2022)

Abstract Background: The ctDNA shedding rate, concentration and stability are associated with tumor type, stage, ctDNA degradation and clearance mechanisms. Tumoral heterogeneity together with tissue of origin related genomic alterations adds complexity to genomic profiling. The value of NGS panels capable of detecting variants in both tissue and ctDNA are well recognized. Therefore, it is essential to assess the comprehensive NGS panel(s) performance in both liquid biopsy and tissue by comparing to tissue WES. In this study, we systematically conducted performance evaluation of llumina TruSight™ Oncology 500 gene (TSO500) NGS assay(s) using matched tissue and ctDNA specimens Methods: Matched tissue and plasma samples from seven treatment naive stage III/IV CRC patients were utilized for Illumina TSO500 sequencing and WES. Tissue samples were separately analyzed by both WES and the TSO500 tissue panel while extracted cfDNA was analyzed by TSO500 ctDNA panel. Illumina BaseSpace TruSight Oncology 500 platform (CombinedVariantOutput.tsv) was applied to select non-synonymous (frameshift, in-frame, nonsense, missense, translation start site, nonstop and splice site) variants in both cfDNA and tissue samples. Genes found to be mutated by tissue WES were filtered for corresponding mutated genes detected by TSO500 analysis. Next, using maftools, we characterize the most frequently mutated genes and the mutations observed for each patient sample. Results: 1,300 variants and 33 copy number variants were observed in the liquid biopsy samples whereas 1,199 variants, 9 genes with high copy number variations and 3 gene fusions were observed in the TSO500 tissue panel. Of these mutations, 889 variants (56.9%) were common between the liquid and tissue in the TSO500 panels. We observed a significant correlation across WES and TSO500-called variants (TSO500 tissue/TSO500 cfDNA r2=0.81, WES/TSO500 tissue r2=0.91 (47 variants), WES/TSO500 cfDNA r2=0.84 (17 variants). In the TSO tissue and cfDNA datasets, 19/20 most commonly mutated genes were the same, while FAT1 was the most commonly mutated gene in both tissue and ctDNA samples. In addition, only 2/20 (APC and TP53) most commonly mutated genes found in the tissue WES dataset were included in the top 20 for two TSO500 datasets. Furthermore, the RTK-RAS pathway had mutations in 22 genes in the liquid and tissue TSO500, by far the most of any pathway. Conclusions: Significant concordance between the TSO500 liquid biopsy and tissue datasets were demonstrated, but lesser concordance with the tissue WES dataset. The evidence supports the potential of leveraging both ctDNA and FFPE based genomic observation to enable precision oncology. A deeper analytical dive into each dataset is on-going. Citation Format: Dennis O'Rourke, Roman Alpatov, Danyi Wang, Zheng Feng, Juergen Scheuenpflug. Comparing comprehensive NGS panel(s) based approach versus tissue whole exome sequencing (WES) using matched tissue and circulating tumor DNA from late-stage colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5105.